Visualizing behaviors of cell populations within living multicellular organisms in real time is of great value to life science but challenging due to the lack of ideal probes. In this work, a biocompatible fluorogen, azide-functionalized tetraphenylethene pyridinium (TPE-PyN3), is reported for noninvasive imaging and sensing within living systems. TPE-PyN3 exhibits unique aggregation-induced emission (AIE) attributes and high affinity to mitochondria, enabling it to achieve specific mitochondrial imaging and long-term cellular observing with excellent photostability both in vitro and in vivo. The high membrane penetrability of TPE-PyN3 allows all of the cells within the living zebrafish embryos to be morphologically visualized and reconstructed in 3D. Moreover, TPE-PyN3 is capable of indicating cell apoptosis because of its sensitivity to the change of mitochondrial membrane potential. The findings presented here provide a simple and noninvasive tool for studying behaviors of cell populations in vivo for the first time by a small-molecule AIE probe.